HL7 FHIR Implementation Guide: Breast Cancer Data, Release 1 - US Realm (Draft for Comment 2)
This page is part of the Breast Cancer Data Logical Models and FHIR Profiles (v0.2.0: STU 1 Draft) based on FHIR R3. . For a full list of available versions, see the Directory of published versions 
The official URL for this profile is:
http://hl7.org/fhir/us/breastcancer/StructureDefinition/cimi-entity-Specimen
A specimen is a substance, physical object, or collection of objects, that the laboratory considers a single discrete, uniquely identified unit that is the subject of one or more steps in the laboratory workflow. A specimen may include multiple physical pieces as long as they are considered a single unit within the laboratory workflow. A specimen results from one to many specimen collection procedures, and may be contained in multiple specimen containers. Specimen may have one or more processing activities.
This profile builds on Specimen.
This profile was published on Fri Aug 17 00:00:00 AEST 2018 as a draft by The HL7 Cancer Interoperability Group sponsored by Clinical Interoperability Council Work Group (CIC).
View the corresponding SpecimenModel logical model.
Summary
Mandatory: 0 element (1 nested mandatory element)
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
BC Mapping Source
This structure represents the following BC mapping definition:
cimi.entity.Specimen maps to Specimen: AccessionIdentifier maps to accessionIdentifier SpecimenStatus maps to status Type maps to type CollectionSource maps to subject CollectionSite.AnatomicalLocation maps to collection.bodySite CollectionMethod.CodeableConcept maps to collection.method SourceSpecimen maps to parent ReceivedTime maps to receivedTime SpecimenContainer.Identifier maps to container.identifier SpecimenContainer.Details maps to container.description SpecimenContainer.Type maps to container.type SpecimenContainer.Capacity maps to container.capacity SpecimenContainer.SpecimenQuantity maps to container.specimenQuantity SpecimenContainer.Additive maps to container.additive[x]
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Specimen | I | 0..* | BC Specimen Profile | |
  id | Σ | 0..1 | id | Logical id of this artifact |
 meta | Σ | 0..1 | Meta | Metadata about the resource |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| language | 0..1 | code | Language of the resource content Binding: Common Languages (extensible) | |
| text | I | 0..1 | Narrative | Text summary of the resource, for human interpretation |
 contained | 0..* | Resource | Contained, inline Resources | |
 extension | 0..* | Extension | Additional Content defined by implementations Slice: Unordered, Open by value:url | |
| cimi-entity-CollectionTime-extension | 0..1 | dateTime, Period | BC CollectionTime Extension URL: http://hl7.org/fhir/us/breastcancer/StructureDefinition/cimi-entity-CollectionTime-extension | |
| cimi-entity-SpecimenTreatment-extension | 0..* | Reference(BC SpecimenTreatment Profile) | BC SpecimenTreatment Extension URL: http://hl7.org/fhir/us/breastcancer/StructureDefinition/cimi-entity-SpecimenTreatment-extension | |
| cimi-entity-HandlingRisk-extension | 0..* | CodeableConcept | BC HandlingRisk Extension URL: http://hl7.org/fhir/us/breastcancer/StructureDefinition/cimi-entity-HandlingRisk-extension | |
| cimi-entity-SpecialHandling-extension | 0..* | CodeableConcept | BC SpecialHandling Extension URL: http://hl7.org/fhir/us/breastcancer/StructureDefinition/cimi-entity-SpecialHandling-extension | |
 modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| identifier | Σ | 0..* | Identifier | External Identifier |
| accessionIdentifier | Σ | 0..1 | AccessionIdentifierProfile | Identifier assigned by the lab |
| status | ?!Σ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required) |
| type | Σ | 1..1 | CodeableConcept | Kind of material that forms the specimen Binding: v2 Specimen Type (required) |
 subject | Σ | 1..1 | Reference(US Core Patient Profile | BC Group Profile | US Core Device Profile | BC Substance Profile) | Where the specimen came from. This may be from the patient(s) or from the environment or a device |
| receivedTime | Σ | 0..1 | dateTime | The time when specimen was received for processing |
| parent | 0..1 | Reference(BC Specimen Profile) | Specimen from which this specimen originated | |
| request | 0..* | Reference(ProcedureRequest) | Why the specimen was collected | |
| collection | I | 0..1 | BackboneElement | Collection details |
 id | 0..1 | string | xml:id (or equivalent in JSON) | |
| extension | 0..* | Extension | Additional Content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| collector | Σ | 0..1 | Reference(Practitioner) | Who collected the specimen |
 collected[x] | Σ | 0..1 | dateTime, Period | Collection time |
| quantity | 0..1 | SimpleQuantity | The quantity of specimen collected | |
| method | 0..1 | CodeableConcept | Technique used to perform collection Binding: FHIR Specimen Collection Method (example) | |
 bodySite | 0..1 | CodeableConcept | Anatomical collection site Binding: BC AnatomicalLocationVS ValueSet (required) | |
| processing | I | 0..* | BackboneElement | Processing and processing step details |
| id | 0..1 | string | xml:id (or equivalent in JSON) | |
| extension | 0..* | Extension | Additional Content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| description | 0..1 | string | Textual description of procedure | |
| procedure | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example) | |
| additive | 0..* | Reference(Substance) | Material used in the processing step | |
| time[x] | 0..1 | dateTime, Period | Date and time of specimen processing | |
| container | I | 0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) |
| id | 0..1 | string | xml:id (or equivalent in JSON) | |
| extension | 0..* | Extension | Additional Content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| identifier | Σ | 0..* | IdentifierProfile | Id for the container |
| description | 0..1 | string | Textual description of the container | |
| type | 0..1 | CodeableConcept | Kind of container directly associated with specimen Binding: SpecimenContainer (example) | |
| capacity | 0..1 | SimpleQuantity | Container volume or size | |
| specimenQuantity | 0..1 | SimpleQuantity | Quantity of specimen within container | |
| additive[x] | 0..1 | CodeableConcept, Reference(BC Substance Profile) | Additive associated with container Binding: v2 Additive/Preservative (example) | |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
Summary
Mandatory: 0 element (1 nested mandatory element)
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
BC Mapping Source
This structure represents the following BC mapping definition:
cimi.entity.Specimen maps to Specimen: AccessionIdentifier maps to accessionIdentifier SpecimenStatus maps to status Type maps to type CollectionSource maps to subject CollectionSite.AnatomicalLocation maps to collection.bodySite CollectionMethod.CodeableConcept maps to collection.method SourceSpecimen maps to parent ReceivedTime maps to receivedTime SpecimenContainer.Identifier maps to container.identifier SpecimenContainer.Details maps to container.description SpecimenContainer.Type maps to container.type SpecimenContainer.Capacity maps to container.capacity SpecimenContainer.SpecimenQuantity maps to container.specimenQuantity SpecimenContainer.Additive maps to container.additive[x]
Differential View
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Specimen | I | 0..* | BC Specimen Profile | |
| id | Σ | 0..1 | id | Logical id of this artifact |
| meta | Σ | 0..1 | Meta | Metadata about the resource |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| language | 0..1 | code | Language of the resource content Binding: Common Languages (extensible) | |
| text | I | 0..1 | Narrative | Text summary of the resource, for human interpretation |
| contained | 0..* | Resource | Contained, inline Resources | |
| extension | 0..* | Extension | Additional Content defined by implementations Slice: Unordered, Open by value:url | |
| cimi-entity-CollectionTime-extension | 0..1 | dateTime, Period | BC CollectionTime Extension URL: http://hl7.org/fhir/us/breastcancer/StructureDefinition/cimi-entity-CollectionTime-extension | |
| cimi-entity-SpecimenTreatment-extension | 0..* | Reference(BC SpecimenTreatment Profile) | BC SpecimenTreatment Extension URL: http://hl7.org/fhir/us/breastcancer/StructureDefinition/cimi-entity-SpecimenTreatment-extension | |
| cimi-entity-HandlingRisk-extension | 0..* | CodeableConcept | BC HandlingRisk Extension URL: http://hl7.org/fhir/us/breastcancer/StructureDefinition/cimi-entity-HandlingRisk-extension | |
| cimi-entity-SpecialHandling-extension | 0..* | CodeableConcept | BC SpecialHandling Extension URL: http://hl7.org/fhir/us/breastcancer/StructureDefinition/cimi-entity-SpecialHandling-extension | |
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| identifier | Σ | 0..* | Identifier | External Identifier |
| accessionIdentifier | Σ | 0..1 | AccessionIdentifierProfile | Identifier assigned by the lab |
| status | ?!Σ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required) |
| type | Σ | 1..1 | CodeableConcept | Kind of material that forms the specimen Binding: v2 Specimen Type (required) |
| subject | Σ | 1..1 | Reference(US Core Patient Profile | BC Group Profile | US Core Device Profile | BC Substance Profile) | Where the specimen came from. This may be from the patient(s) or from the environment or a device |
| receivedTime | Σ | 0..1 | dateTime | The time when specimen was received for processing |
| parent | 0..1 | Reference(BC Specimen Profile) | Specimen from which this specimen originated | |
| request | 0..* | Reference(ProcedureRequest) | Why the specimen was collected | |
| collection | I | 0..1 | BackboneElement | Collection details |
| id | 0..1 | string | xml:id (or equivalent in JSON) | |
| extension | 0..* | Extension | Additional Content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| collector | Σ | 0..1 | Reference(Practitioner) | Who collected the specimen |
| collected[x] | Σ | 0..1 | dateTime, Period | Collection time |
| quantity | 0..1 | SimpleQuantity | The quantity of specimen collected | |
| method | 0..1 | CodeableConcept | Technique used to perform collection Binding: FHIR Specimen Collection Method (example) | |
| bodySite | 0..1 | CodeableConcept | Anatomical collection site Binding: BC AnatomicalLocationVS ValueSet (required) | |
| processing | I | 0..* | BackboneElement | Processing and processing step details |
| id | 0..1 | string | xml:id (or equivalent in JSON) | |
| extension | 0..* | Extension | Additional Content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| description | 0..1 | string | Textual description of procedure | |
| procedure | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example) | |
| additive | 0..* | Reference(Substance) | Material used in the processing step | |
| time[x] | 0..1 | dateTime, Period | Date and time of specimen processing | |
| container | I | 0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) |
| id | 0..1 | string | xml:id (or equivalent in JSON) | |
| extension | 0..* | Extension | Additional Content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| identifier | Σ | 0..* | IdentifierProfile | Id for the container |
| description | 0..1 | string | Textual description of the container | |
| type | 0..1 | CodeableConcept | Kind of container directly associated with specimen Binding: SpecimenContainer (example) | |
| capacity | 0..1 | SimpleQuantity | Container volume or size | |
| specimenQuantity | 0..1 | SimpleQuantity | Quantity of specimen within container | |
| additive[x] | 0..1 | CodeableConcept, Reference(BC Substance Profile) | Additive associated with container Binding: v2 Additive/Preservative (example) | |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
Downloads: StructureDefinition: (XML, JSON, TTL), Schema: XML Schematron
| Path | Name | Conformance | ValueSet |
| Specimen.language | Common Languages | extensible | Common Languages |
| Specimen.status | SpecimenStatus | required | SpecimenStatus |
| Specimen.type | v2 Specimen Type | required | v2 Specimen Type |
| Specimen.collection.method | FHIR Specimen Collection Method | example | FHIR Specimen Collection Method |
| Specimen.collection.bodySite | BC AnatomicalLocationVS ValueSet | required | AnatomicalLocationVS |
| Specimen.processing.procedure | SpecimenProcessingProcedure | example | SpecimenProcessingProcedure |
| Specimen.container.type | SpecimenContainer | example | SpecimenContainer |
| Specimen.container.additive[x] | v2 Additive/Preservative | example | v2 Additive/Preservative |
| Id | Path | Details | Requirements |
| dom-2 | Specimen | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-1 | Specimen | If the resource is contained in another resource, it SHALL NOT contain any narrative : contained.text.empty() | |
| dom-4 | Specimen | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
| dom-3 | Specimen | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource : contained.where(('#'+id in %resource.descendants().reference).not()).empty() | |
| ele-1 | Specimen.collection | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
| ele-1 | Specimen.processing | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) | |
| ele-1 | Specimen.container | All FHIR elements must have a @value or children : hasValue() | (children().count() > id.count()) |
